Q9SHE7 (RUB1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin-NEDD8-like protein RUB1

Cleaved into the following 2 chains:

1. Ubiquitin
2. NEDD8-like protein RUB1
   Alternative name(s):
   Ubiquitin-related protein 1
   Short name=AtRUB1

Gene names

Name:	RUB1
Synonyms:	NEDD8, UBQ15
Ordered Locus Names:	At1g31340
ORF Names:	T19E23.13

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	156 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling By similarity. Ref.5 Ref.6 NEDD8-like protein RUB1: Appears to function as a stable post-translational protein modifier. An AMP-RUB1 intermediate is formed by an activating enzyme, distinct from the ubiquitin activating enzyme E1, which is composed of a heterodimer AXR1/ECR1. Auxin response is mediated, at least in part, through modification of the cullin AtCUL1 by the attachment of RUB1 to 'Lys-692'. Ref.5 Ref.6
Subunit structure	NEDD8-like protein RUB1: Forms a thiol ester with the heterodimer AXR1/ECR1, specifically with the 'Cys-215' of ECR1.
Subcellular location	Ubiquitin: Cytoplasm By similarity. Nucleus By similarity.
Tissue specificity	Expressed in leaves, stems and flowers. Ref.8
Miscellaneous	Ubiquitin is encoded by 16 different genes. Ubiquitin is generally synthesized as a polyubiquitin precursor with tandem head to tail repeats. Often, there is one to three additional amino-acids after the last repeat, removed in the mature protein. Alternatively, ubiquitin extension protein is synthesized as a single copy of ubiquitin fused to a ribosomal protein (either L40 or S27A) or to an ubiquitin-related protein (either RUB1 or RUB2). Following translation, extension protein is cleaved from ubiquitin.
Sequence similarities	Belongs to the ubiquitin family. Contains 2 ubiquitin-like domains.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Cellular component	Cytoplasm Nucleus
Domain	Repeat
PTM	Isopeptide bond Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	embryo development Inferred from genetic interaction PubMed 15319484. Source: TAIR ethylene biosynthetic process Inferred from mutant phenotype PubMed 15319484. Source: TAIR protein neddylation Traceable author statement PubMed 10322542. Source: TAIR response to auxin stimulus Traceable author statement Ref.5. Source: TAIR
Cellular_component	cytosol Inferred from direct assay PubMed 21166475. Source: TAIR nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membrane Inferred from direct assay PubMed 17644812. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 76

76

Ubiquitin

PRO_0000396910

Chain

77 – 152

76

NEDD8-like protein RUB1

PRO_0000035965

Propeptide

153 – 156

4

Probable

PRO_0000035966

Regions

Domain

1 – 76

76

Ubiquitin-like 1

Domain

77 – 152

76

Ubiquitin-like 2

Amino acid modifications

Cross-link

11

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7

Cross-link

29

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7

Cross-link

33

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7

Cross-link

48

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7

Cross-link

63

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7

Cross-link

76

Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) By similarity

Cross-link

152

Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) By similarity

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

156

Helix Strand Turn

Details...

Beta strand

79 – 82

4

Beta strand

88 – 92

5

Helix

99 – 110

12

Helix

114 – 116

3

Beta strand

117 – 121

5

Helix

133 – 135

3

Beta strand

142 – 147

6

Sequences

	Sequence		Length	Mass (Da)
	Q9SHE7 [UniParc]. Last modified August 10, 2010. Version 3. Checksum: FA8D702BB9C1B3AE	FASTA	156	17,397
	10 20 30 40 50 60 MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLADYN 70 80 90 100 110 120 IQKESTLHLV LRLRGGTMIK VKTLTGKEIE IDIEPTDTID RIKERVEEKE GIPPVQQRLI 130 140 150 YAGKQLADDK TAKDYNIEGG SVLHLVLALR GGFGLL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[2]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[3]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[4]	"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs." Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K. , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K. Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"The ubiquitin-related protein RUB1 and auxin response in Arabidopsis." del Pozo J.C., Timpte C., Tan S., Callis J., Estelle M. Science 280:1760-1763(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH AXR1 AND ECR1.
[6]	"The Arabidopsis cullin AtCUL1 is modified by the ubiquitin-related protein RUB1." del Pozo J.C., Estelle M. Proc. Natl. Acad. Sci. U.S.A. 96:15342-15347(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants." Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K. Mol. Cell. Proteomics 6:601-610(2007) [PubMed] [Europe PMC] [Abstract] Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-11; LYS-29; LYS-33; LYS-48 AND LYS-63, MASS SPECTROMETRY. Strain: cv. Landsberg erecta.
[8]	"The rub family of ubiquitin-like proteins. Crystal structure of Arabidopsis rub1 and expression of multiple rubs in Arabidopsis." Rao-Naik C., delaCruz W., Laplaza J.M., Tan S., Callis J., Fisher A.J. J. Biol. Chem. 273:34976-34982(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 79-152, TISSUE SPECIFICITY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AC007654 Genomic DNA. Translation: AAF24594.1.
CP002684 Genomic DNA. Translation: AEE31344.1.
BT005749 mRNA. Translation: AAO64156.1.
BT006110 mRNA. Translation: AAP04095.1.
AK228591 mRNA. Translation: BAF00506.1.

IPI

IPI00544216.

PIR

C86439.

RefSeq

NP_564379.2. NM_102873.4.

UniGene

At.25337.
At.30783.
At.43046.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BT0	X-ray	1.70	A	79-152	[»]

ProteinModelPortal

Q9SHE7.

SMR

Q9SHE7. Positions 1-152.

ModBase

Search...

Proteomic databases

PaxDb

Q9SHE7.

PRIDE

Q9SHE7.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT1G31340.1; AT1G31340.1; AT1G31340.

GeneID

840023.

KEGG

ath:AT1G31340.

Organism-specific databases

TAIR

At1g31340.

Phylogenomic databases

eggNOG

COG5272.

KO

K12158.

OMA

INIEPND.

PhylomeDB

Q9SHE7.

ProtClustDB

CLSN2688712.

Gene expression databases

Genevestigator

Q9SHE7.

GermOnline

AT1G31340. Arabidopsis thaliana.

Family and domain databases

InterPro

IPR000626. Ubiquitin.
IPR019954. Ubiquitin_CS.
IPR019956. Ubiquitin_subgr.
IPR019955. Ubiquitin_supergroup.
[Graphical view]

Pfam

PF00240. ubiquitin. 2 hits.
[Graphical view]

PRINTS

PR00348. UBIQUITIN.

SMART

SM00213. UBQ. 2 hits.
[Graphical view]

PROSITE

PS00299. UBIQUITIN_1. 2 hits.
PS50053. UBIQUITIN_2. 2 hits.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9SHE7.

Entry information

Entry name

RUB1_ARATH

Accession

Primary (citable) accession number: Q9SHE7
Secondary accession number(s): O80715 , P59263, Q0WQU3, Q38875, Q9LDJ2, Q9LYW1, Q9M0W3, Q9M1P9, Q9S7X3

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 31, 2003
Last sequence update:	August 10, 2010
Last modified:	May 1, 2013
This is version 89 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program